Proceedings of the 15th Annual MCBIOS Conference

Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference

Authors: Jonathan D. Wren, Robert J. Doerkson, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda and Shraddha Thakkar

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM...

Authors: Philip Berg, Evan W. McConnell, Leslie M. Hicks, Sorina C. Popescu and George V. Popescu

Similarities and differences between variants called with human reference genome HG19 or HG38

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38....

Authors: Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong and Huixiao Hong

Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion

Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of t...

Authors: Sujoy Roy, Kazi I. Zaman, Robert W. Williams and Ramin Homayouni

Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk

Barrett’s esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor f...

Authors: Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng and Mohammed Orloff

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations

The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments...

Authors: Aleksandra I. Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh and Jonathan D. Wren

Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions

Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses ...

Authors: Norbert Bokros, Sorina C. Popescu and George V. Popescu

Local edge-enhanced active contour for accurate skin lesion border detection

Dermoscopy is one of the common and effective imaging techniques in diagnosis of skin cancer, especially for pigmented lesions. Accurate skin lesion border detection is the key to extract important dermoscopic...

Authors: Mustafa Bayraktar, Sinan Kockara, Tansel Halic, Mutlu Mete, Henry K. Wong and Kamran Iqbal

Partition-based optimization model for generative anatomy modeling language (POM-GAML)

This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear opt...

Authors: Doga Demirel, Berk Cetinsaya, Tansel Halic, Sinan Kockara and Shahryar Ahmadi

Predicting protein residue-residue contacts using random forests and deep networks

The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact predictio...

Authors: Joseph Luttrell IV, Tong Liu, Chaoyang Zhang and Zheng Wang

Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA

Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP),...

Authors: Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen Harris, Shraddha Thakkar, Guangxu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong and Hong Fang

Keanu: a novel visualization tool to explore biodiversity in metagenomes

One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing F...

Authors: Adam Thrash, Mark Arick II, Robyn A. Barbato, Robert M. Jones, Thomas A. Douglas, Julie Esdale, Edward J. Perkins and Natàlia Garcia-Reyero